Specifying the African Origins of the Afro Diasporan Genome (part 2)

Schroeder et al. (2015) Fig1 B&C

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean (Schroeder et al., 2015)

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“The transatlantic slave trade resulted in the forced movement of over 12 million Africans to the Americas. Although many coastal shipping points are known, they do not necessarily reflect the slaves’ actual ethnic or geographic origins. We obtained genome-wide data from 17th-century remains of three enslaved individuals who died on the Caribbean island of Saint Martin and use them to identify their genetic origins in Africa, with far greater precision than previously thought possible. The study demonstrates that genomic data can be used to trace the genetic ancestry of long-dead individuals, a finding that has important implications for archeology, especially in cases where historical information is missing.” (Schroeder et al., 2015, p.3669)

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Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

(Schroeder et al., 2015)
Link to online article

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ADMIXTURE Analysis […]The distribution of these components in our samples indicates that STM1 has a higher proportion of Bantu-specific ancestry, whereas STM2 and STM3 carry higher proportions of the component prevalent among the non-Bantu–speaking Yoruba, Brong, and Igbo. Notably, STM2 also shows a slightly higher proportion of the component prevalent among the Kaba, Mada, and Bulala, perhaps suggesting closer affinity with Chadic or Sudanic speakers” (Schroeder et al., 2015, p.3671)

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Schroeder et al. (2015) Fig1 D

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean (Schroeder et al., 2015)

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This 2015 study is truly showcasing how DNA research has made exciting progress in uncovering the origins of enslaved Africans relocated to the Americas. In this case even involving 3 individuals who lived in the 17th century! Their real names remain unknown regrettably but in the study they are referred to as STM1, STM2 & STM3 as they were buried on the Dutch Caribbean island of Sint-Maarten. The extraction of ancient DNA is increasingly getting more sophisticated and holds great promises for future research. It goes without saying that ethical considerations should always be a part of this kind of research.There are several locations of African slave burial grounds known throughout the Americas, such as the infamous “New Blacks” cemetery in Rio de Janeiro but also a Mexican archaelogical site in Campeche where the oldest remains of Africans in the Americas were found (dating from the 1500’s). Then there’s of course the African Burial Ground in New York. For the Africans buried in New York a very extensive report has already been published in 2009 based mostly on dental and cranial analysis but also mtDNA data was extracted (see chapter 5, page 89  “Origins of the New York African Burial Ground Population“). That report wasn’t able to draw any real conclusions yet given the state of knowledge at that time but undoubtedly it would be enhanced by an additional autosomal analysis as performed in this present study from 2015.

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Schroeder et al. (2015) Supplement, Fig.S20, Treemix

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean (Schroeder et al., 2015, Supplement)

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“Genome-wide analyses clearly bear great potential to predict a person’s place of origin, but we caution that there are also limitations.” (Schroeder et al., 2015, p.3671)

Overlap with Bryc et al.’s African data set
For the more fine-scaled analyses, we used a previously published dataset (79) consisting of 146 African individuals genotyped on the Affymetrix GeneChip Human Mapping 500K array set. The dataset includes individuals from 11 different African populations including: Bamoun (20), Brong (8), Bulala (15), Fang (18), Hausa (13), Igbo (17), Kaba (16), Kongo (9), Mada (12), Fulani (13) and Xhosa (5). In addition, the dataset includes 57 Yoruba individuals from the HapMap Project (79, 80), adding to a total of 203 individuals covering 351,753 SNPs..” (Schroeder et al., 2015, supplement, p.14)

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Despite its spectacular findings and innovative use of ancient DNA, this study also illustrates some of the remaining obstacles of DNA research. When it comes to their HGDP dataset of African sampling, there’s really no improvement over the 2009 studies i reviewed earlier (Specifying the African origins of the African American genome). Their autosomal analysis and number of African reference populations looks quite similar to Bryce et al. (2009) especially. Aside from the question of how to obtain high resolution samples of ancient DNA we also have to take into account that modernday African DNA samplegroups are not going to be a perfect equivalent of historical source populations. Between the 1600’s and our present era plenty of interethnic geneflow and migrations might have taken place which could have significantly altered the ancestral composition of ethnic groups living three centuries ago.

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Y-DNA of STM1 evidence of northern Cameroonian origins?

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“[..] we note that haplogroup L3b1a is one of the most common lineages found in the Lake Chad Basin (23).This finding is noteworthy, because the Y-chromosome lineage of this individual (STM1) was identified as belonging to haplogroup R1b1c-V88, which—although quite rare in Africa on the whole—occurs at extremely high frequency in the Lake Chad Basin, rising to 95% in one population of northern Cameroon” […]

“Taken together, the genetic data suggest that STM1 may have originated among Bantu-speaking groups in northern Cameroon, whereas STM2 and STM3 more likely originated among non-Bantu speakers living in present-day Nigeria and Ghana.” (Schroeder et al., 2015, p.3671). (Schroeder et al., 2015, p.3671).

“Thus, the paternal inheritance of STM1 strongly supports a homeland near the meeting-points of Cameroon, Nigeria, Niger, and Chad.” (Schroeder et al., 2015, supplement, p.13).

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Schroeder et al. (2015) Table 1

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean (Schroeder et al., 2015)

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Cruciani et al. 2010 (R1b-V88 frequencies, map)

Human Y chromosome haplogroup R-V88 – a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages (Cruciani et al. 2010)

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Besides a genomewide autosomal analysis this study also determined the uniparental markers of the three African captives buried in Sint Maarten. When it comes to the 3 maternal haplogroups they identified they make the following remark:

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Tracing these lineages to particular regions in Africa is challenging because of their pan-continental distribution, which is the result of thousands of years of population movements (e.g., the Bantu migrations) and continued gene flow“.  (Schroeder et al., 2015, p.3671).

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Apparently the Y-DNA for STM2 could not be established but the regionally restricted Y-DNA for STM1 presents a singular case whereby haplogroups can indeed be used to predict a likely ancestral location. The authors of the study were very lucky to have come across such an example when only 3 individuals were examined.

From a 2010 study named “Human Y chromosome haplogroup R-V88 – a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages” (Cruciani et al. 2010) we get some idea of the distribution of this quite unique haplogroup within Africa. Generally speaking R1b being much more prevalent in Europe! See this map for a global distribution. Below can be seen an overview of Cruciani’s et al. (2010) findings, we can see that this haplogroup’s frequency indeed peeks among northern Cameroonian populations, however they are all mostly Chadic speaking and none of them Bantu speaking. STM1’s haplogroup is however also found with decreased frequency among the Yoruba and the southern Cameroonian ethnic group of the Ewondo. Of course there’s still many missing ethnic groups being sampled and also looking at the sometimes very minor sample size it’s obvious this overview still has many limitations eventhough it’s been very valuable in itself.

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Cruciani et al. 2010 (R1b-V88 frequencies)

Human Y chromosome haplogroup R-V88 – a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages (Cruciani et al. 2010)

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Given that the autosomal analysis for STM1 showed an increased Bantu affinity and not so much Chadic (which was instead detected for STM2) we should perhaps be careful to assume a northern Cameroonian origin right away. Even with both of his haplogroups (also his mtDNA L3b1a is being said to be most frequent around Lake Chad) pointing to a more northern origin, as this could very well also be a legacy of geneflow which took place centuries before STM1 was shipped to Sint Maarten. With the autosomal evidence pointing in a different direction it’s again a reminder how haplogroups can only specify a very minor part of a person’s ancestry. The authors of this study mention repeatedly that STM1 could hail from “Bantu-speaking groups from northern Cameroon”. However judging from the ethnolinguistic maps i posted over here and also in the Lower Guinea section, Bantu speaking groups only live in southern Cameroon! In fact from the above overview it’s also only the Ewondo who are shown as Bantu speaking while all the other Cameroonian groups with STM1’s haplogroup are Chadic, Semetic, Atlantic, Saharan, Adamawa speaking instead. Given that they only sampled 3 Bantu speaking groups from southern Cameroon i suppose it could be possible that STM1’s haplogroup of R1b1c-V88 could still be found in other parts of southern Cameroon as well.

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Early example of inland reach of slave trade?

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Schroeder et al. (2015) Supplement, Fig.S21 Admixture analysis

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean (Schroeder et al., 2015, Supplement)

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Despite a perhaps not so clear-cut case for (recent) northern Cameroonian origins afterall it’s still fascinating to speculate on the inland reach of slave trade as also suggested by the above ADMIXTURE analysis of these 3 individuals from Sint Maarten. Eventhough the study proposes different ethnic origins for the three of them i find it striking that in above figure at K=6 their ancestral composition doesn’t seem that distinct from one another and could possibly be explained by individual variation within 1 (not yet sampled) ethnic group or else 2 or 3 neighbouring ethnic groups. Intriguingly all three of them show minor bits of red “Bulala”, yellow “Mada” and orange “Hausa” components. Such combination only shown consistently by the Kaba (from Chad), although their red “Bulala” is relatively higher. Looking at the light blue/dark blue ratio it seems rather that the Igbo come closest. I’m sure it’s much more complex than this ad hoc method 😉 but could above ADMIXTURE analysis perhaps be suggesting ethnic origins located inbetween the Igbo and Kaba, say somewhere in Nigeria’s Middle Belt?

Generally speaking historians have made the assumption that slave trade routes reaching far into the interior of West Africa only developed in the later periods of Trans Atlantic Slave Trade, because of ever rising demand by European buyers as well as increased warfare involving Jihadist empires. The authors of the study mention that only 1 slavevoyage to Sint Maarten has been recorded for the relevant timeperiod, however without any useful details on its provenance. These 3 enslaved Africans living in the Dutch ruled part of Sint Maarten would have been brought there by Dutch vessels in all likelyhood, probably after a stop at Curacao, which was the main slavetrading hub for the Dutch in the Caribbean.  If we look into the slave trade patterns of the Dutch around this period (1600-1700) we can see that according to both contemporary testimony as well as documented records, the Bight of Benin was clearly a more frequently visited slaving area than the Bight of Biafra.

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TAST

Trans-Atlantic Slave Trade Database (http://www.slavevoyages.org/)

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From a very valuable slave narrative written down in 1850 in Sierra Leone we know that enslaved people from around the Lake Chad area would at times be transported not directly to the south onwards to the Bight of Biafra but instead first were transported west along Hausa trading routes via Kano and only then southwards to the Bight of Benin (Curtin, 1968). This testimony came from Ali Eisami, born near Bornu in presentday northeastern Nigeria (see also this article). He was a Kanuri speaker, one of the populations sampled by Cruciani et al. (2010). Other socalled Liberated Africans brought to Sierra Leone and being interviewed about their origins also tell us about the inland reach of slave trade within Nigeria & Cameroon in this later period. See for example this map below showing several ethnicities around Lake Chad but also many from the Cameroon Highlands and the Nigerian Middle Belt. Also in the 1815 Slave Register of Saint Lucia there’s one person of Bornu being mentioned out of 3,488 African born slaves. Indicating that they might not have been numerous but still were present. The Bight of Biafra label is a modernday addition btw by Higman. As evidenced by Ali Eiami a person from Bornu could also very well have been shipped from a Bight of Benin port.

Higman

St. Lucia Slave register 1815 (Higman, 1984)

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Nigeria Cameroon mapsl

Taken from “The Atlantic Slave Trade: A Census” (Curtin, 1969)

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It’s not clear which route would have been preferred for transporting captives from interior parts of eastern Nigeria/northern Cameroon to the coastal areas for transatlantic shipment. For the Bight of Benin we have additional evidence that also many Hausa slaves were shipped via Benin to Brazil, while for the Bight of Biafra we know that an overwelming majority of captives shipped from this area were known simply as either “Eboe” or “Moco”, implying ethnic origins near the coast. However this might still obscure the presence of  additional interior captives being forced to assume a new umbrella identity. As much is also implied by this below quote from the 1699 travelling account of French slave trader James Barbot who knew the Igbo’s under the name of “Hackbous” and said they were:

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 “a people much addicted to war and preying on their neighbours to the northward, and are themselves lusty tall men.” (Hair, 1992, p.693)

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It’s noteworthy that this quote above was made not too long after the enslavement of the 3 Sint Maarten captives took place. Also despite that the Dutch clearly preferred the Bight of Benin over the Bight of Biafra it was mostly in the 1600’s that they visited this area at all. In later timeperiods they seem to have abandoned all trading with the Bight of Biafra. A perhaps totally unrelated trivial detail about STM2 still also comes to mind:

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 “Skeleton number two (STM2) belonged to an older male who would have been approximately 35-40 years old at the time of death. […]The size of the long bones suggests that this individual had been a very tall person, with a calculated stature of about 190 cm.”

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All three persons had filed teeth btw, a common practice among many African ethnic groups, and often commented upon by contemporary Europeans. Although they might originally have been used as ethnic markers still the authors believe that:

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“Similar types of dental modification are known from Africa but it is difficult to be more specific because the designs, especially some of the more common ones, were used by several groups (35-39). The W-shaped pattern used in case of STM2 (Fig. S3) appears to have been fairly common, as it has been reported from several parts of Africa (5-8). The design used in case of STM1 (Fig. S2) seems to have been less common but it was also used by several groups, including the Bakongo, the Loango and others (6). Unfortunately, the dentition of STM3 was incomplete so that it was not possible to identify a specific pattern. But in any case it seems clear that, as Witkin (10) rightly points out, the modifications on their own cannot be used to suggest points of origin or specific tribal affiliations.” (Schroeder et al., 2015, Supplement, p.3)

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As a final consideration it’s interesting to take another look at the frequencies of that rare Y-DNA haplogroup of STM1, but this time within the Americas! I wasn’t able to find any reference of haplogroup R1b1c-V88,being found among African American males, however in this below overview taken from Simms et al. (2012) there’s a perhaps telling comparison being made between Jamaica and Haiti. Sampling is obviously limited but R1b-V88* is being shown at a frequency of 4.88% in Haiti and only 0.63% in Jamaica while R1b-M18 is at 0.63% in Jamaica as well, but not detected in Haiti. Generally speaking of course Haiti is known to have had a higher importation rate from the Bight of Benin and Jamaica for the Bight of Biafra (see the Slave Voyages Database). So maybe this is again indicative of preferred coastal outlets of inland slave trading near the Lake Chad area. But it’s admittedly very circumstantial.

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haiti_jamaica

Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow (Simms et al., 2012).

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Sources:

– Cruciani et al. (2010). Human Y chromosome haplogroup R-V88 – a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. European Journal of Human Genetics, 18, 800–807.
– Curtin, P.D. (1968). Africa Remembered: Narratives by West Africans from the era of the Slave Trade.
– Curtin, P.D. (1969). The Atlantic Slave Trade: A Census.
– Hair, P.E.H. (1992). Barbot on Guinea: The Writings of Jean Barbot on West Africa 1678-1712
– Higman, B. W. (1984). Slave populations of the British Caribbean, 1807-1834.
– Simms et al. (2012). Y-chromosomal diversity in Haiti and Jamaica: contrasting levels of sex-biased gene flow. Am J Phys Anthropol 148, (4), 618–631.

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2 gedachten over “Specifying the African Origins of the Afro Diasporan Genome (part 2)

  1. Utilizing this method (GWA), i’d say within the next five years the Big3 could likely predict African ethnicity at 95% confident level. GREAT BLOG! Thank you!

    Liked by 1 persoon

  2. Thanks! I was especially amazed that they were able to utilize this type of analysis on people who were born almost 4 centuries ago!

    Like

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